latex

There are numerous ways to include formatted code in a LaTeX document. Here’s my favourite. Nothing original or clever here, just brief notes for my (and perhaps, your) benefit. Based largely on this how-to.Read the rest…

Ubuntu/jaunty rocks, on the whole. However, to prove that newer does not always equal better, they threw in a couple of shockers. The first is the upgrade from the excellent Amarok 1.4 to the completely-broken 2.0. Head here to repair the damage.

Kile is by far my favourite LaTeX editor and suffered, though not as badly, in the upgrade from 2.0 to 2.1. Reports of various problems litter the web; in my case I see broken toolbar buttons that do nothing when clicked. This fix is much simpler. Just “sudo apt-get remove kile”, scroll to the bottom of the intrepid package page, choose your architecture, download the deb file and “sudo dpkg -i kile_2.0.1-1ubuntu1_i386.deb”. I had no dependency problems and it works just fine.

Finally – open up Synaptic, find kile and from the Package menu item select “lock package”, to prevent future upgrades.

Update: a few days after writing this, an apt-get dist-upgrade upgraded my Kile to 2.1 (despite the “lock package”). However, the broken buttons issue is now fixed for me. Go figure…

All these people finishing their theses takes me back to my own Ph.D. thesis writing experience. Not that I recall much about it at all; rather like giving birth, the memory erases the excruciating pain and substitutes a kinder, gentler version.Read the rest…

I recently asked the FriendFeed community about wiki usage and was struck by a comment from Allyson:

I think we’re on our third incarnation of various bits of wiki software, and we’ve finally hit on the right software for both our wet lab and bioinformaticians

By “the right software”, she means software that makes sense to the people who use it. When faced with several software alternatives, we often find there is one which for some reason, “makes sense” – it meshes naturally with the way our brains work. When you find a program that you like, it’s not only a joy to use but can enable understanding of data and processes that previously eluded you. In other words, good software doesn’t shield you from the fundamentals – it illuminates them.
Here are three examples of software that made me say: “Oh right! Now I get it.” These are not recommendations and opinions expressed are highly subjective: the point is, I like them because they work for me.Read the rest…

Last year I wrote a short post with some ideas on how to generate citation styles. The idea being that whilst there are many styles of referencing in different journals, there is a finite set of elements: plain, bold or italic; all authors or et al. after 3; volume + number or just volume and so on and so on. Computationally, it should be possible to construct a set of questions based on these elements and have a style pop out the other end.

Well, since then I’ve moved to LaTeX and of course, it does precisely this for you. Just “latex makebst”, answer a long series of questions and you’ve got a custom .bst file. More details are available at the LaTeX Bibliography Styles Database.